make_prg A tool to create and update PRGs for input to Pandora from a set of Multiple Sequence Alignments. Location and version: 1 2 3 4 $ which make_prg /local/cluster/bin/make_prg $ make_prg --version 0.3.0 help message: 1 2 3 4 5 6 7 8 9 10 11 12 13 $ make_prg --help usage: make_prg <subcommand> <options> Subcommand entrypoint optional arguments: -h, --help show this help message and exit -V, --version show program's version number and exit Available subcommands: from_msa Make PRG from multiple sequence alignment dir update Update PRGs given new sequences output by pandora.

panX: microbial pan-genome analysis and exploration Overview: panX is a software package for microbial pan-genome analysis, visualization and exploration. The analysis pipeline is based on DIAMOND, MCL and phylogeny-aware post-processing. It takes a set of annotated bacterial strains as input (e.g. NCBI RefSeq records or user’s own data in GenBank format). All genes from all strains are compared to each other via DIAMOND and then clustered into orthologous groups using MCL and adaptive phylogenetic post-processing, which split distantly related genes and paralogs if necessary.

STAR 2.7.9a - Spliced Transcripts Alignment to a Reference Abstract Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. Results: To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure.

Falco: FastQC Alternative Code This program is an emulation of the popular FastQC software to check large sequencing reads for common problems. Location and version: 1 2 3 4 $ which falco /local/cluster/bin/falco $ falco --version falco 0.3.0 help message: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 $ falco --help Usage: falco [OPTIONS] <seqfile1> <seqfile2> .

The Extensive de novo TE Annotator (EDTA) This package is developed for automated whole-genome de-novo TE annotation and benchmarking the annotation performance of TE libraries. The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.

SKESA: strategic k-mer extension for scrupulous assemblies SKESA is a de-novo sequence read assembler for microbial genomes. It uses conservative heuristics and is designed to create breaks at repeat regions in the genome. This leads to excellent sequence quality without significantly compromising contiguity. If desired, SKESA contigs could be connected into a GFA graph using GFA connector. SAUTE: sequence assembly using target enrichment SAUTE is a de Bruijn graph based target enriched de-novo assembler designed for assembling genomic and RNA-seq reads sequenced using Illumina.